Multidisciplinary studies - including clinical, immunologic, pathologic, epidemiologic and molecular genetic investigations - are being used to complement findings in each area and overcome limitations inherent in each approach. Current studies are focusing on: exploring possible environmental risk and protective factors; identifying genetic risk and protective factors by candidate gene and whole genome SNP and sequencing analyses; defining the associations among clinical, laboratory and immunologic features of autoimmune diseases for diagnostic, prognostic and pathogenic purposes; and understanding differences in epigenetics, gene expression and proteomic patterns between monozygotic twins discordant for disease. Evaluation of exposures to silica, organic solvents and other xenobiotics, ultraviolet light, vaccinations, selected drugs and dietary supplements, hormones and pregnancy, tobacco smoke, stressful life events and infectious agents in the development of systemic autoimmune diseases are being conducted via a study of twins and close siblings discordant for systemic autoimmune disease. A group of poorly-understood, life-threatening autoimmune muscle diseases called the myositis syndromes or idiopathic inflammatory myopathies (IIM) are defined by chronic muscle inflammation and weakness and are associated with specific autoantibodies. The major forms of myositis are polymyositis, in which multiple muscles are affected by inflammation, and dermatomyositis, in which patients also develop skin inflammation. Yet there appear to be other types of myositis based on the clinical presentations, pathology and autoantibodies. We are studying both the adult (IIM) and juvenile (JIIM) forms of these diseases to understand possible differences in pathogenesis and risk factors. We recently examined 3 myositis autoantibodies in JIIM that have been associated with more severe phenotypes in adult patients. Autoantibodies recognizing 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) were identified in 1.1% of juvenile myositis patients in a larger registry of more than 400 patients. None had taken statin medications. All patients with anti-HMGCR autoantibodies had immune-mediated necrotizing myopathy, severe proximal and distal weakness, muscle atrophy, joint contractures, and arthralgias, had only partial responses to multiple immunosuppressive medications, and their disease often took a chronic course. The DRB1*07:01 allele was uniformly present, which differed from the DRB1*11:01 risk factor allele in adult patients. Anti-NT5C1A autoantibodies were present in 27% patients with juvenile myositis. As in adults with inclusion body myositis, juvenile myositis patients with anti-NT5C1A autoantibodies had a more severe phenotype, with greater pulmonary symptoms at diagnosis, more frequent hospitalizations, and required a larger number of medications. We also observed anti-Ro52 autoantibodies in the sera of 15% of JIIM patients. Anti-Ro52 is increased in frequency in patients with anti-synthetase or anti-MDA5 autoantibodies, but Ro52 antibodies are also independently associated with interstitial lung disease. Patients with juvenile myositis and anti-Ro52 autoantibodies more often have a chronic illness course and require more medications. One area of investigation in which we have made recent advances involves identifying new genetic associations with juvenile and adult IIM. To accomplish this goal, we formed collaborations with many investigators around the world called the Myositis Genetic Consortium (MYOGEN). Using samples from MYOGEN, we performed a genome-wide association study (GWAS) of adult and juvenile myositis patients of European ancestry and controls. To identify genetic risk factors, we conducted GWAS of the major myositis phenotypes in adult dermatomyositis, juvenile dermatomyositis; polymyositis, and adult dermatomyositis, juvenile dermatomyositis or polymyositis patients with anti-histidyl-tRNA synthetase (anti-Jo-1) autoantibodies, and compared them with controls. Single-nucleotide polymorphisms showing strong associations (P < 5 X 10-8) in GWAS were identified in the major histocompatibility complex (MHC) region for all myositis phenotypes together, as well as for the four clinical and autoantibody phenotypes studied separately. Imputation and regression analyses found that alleles comprising the human leukocyte antigen (HLA) 8.1 ancestral haplotype (AH8.1) defined essentially all the genetic risk in the phenotypes studied. Although the HLA DRB1*03:01 allele showed stronger associations with adult and juvenile dermatomyositis, and HLA B*08:01 with polymyositis and anti-Jo-1 autoantibody-positive myositis, multiple alleles of AH8.1 were required for the full risk effects. Our findings establish that alleles of the AH8.1 comprise the primary genetic risk factors associated with the major myositis phenotypes in geographically diverse Caucasian populations. These studies have found that genes associated with other autoimmune diseases are also seen in myositis phenotypes. Additional HLA associations were seen with myositis specific autoantibodies in the Immunochip studies, including HLA DRB1*03:01 associated with NT5c1A autoantibodies, DRB1*07:01with anti-Mi-2 autoantibodies, and DQB1*02:02 associated with anti-TIF1 autoantibodies in adult patients, while DQB1*02:01 was associated with anti-TIF1 in children. We are continuing these investigations using Immunochip and other approaches and assessing additional phenotypes. We have examined environmental factors as risk factors for myositis and for flares of myositis. Tobacco smoking has been associated with clinical and autoantibody myositis phenotypes in Caucasians. Caucasian ever-smokers were more likely to have polymyositis (PM) (adjusted odds ratio, OR = 2.24), and anti-Jo-1 autoantibodies (adjusted OR = 1.94) and less likely to have anti-p155/140 autoantibodies (adjusted OR = 0.36). Similar trends were present in a pack-year analysis. In Caucasians, ever-smokers had a greater interstitial lung disease (ILD) frequency than never-smokers. In Caucasians, ever-smokers with HLA-DRB1*03:01 allele had the highest odds of PM, ILD, and anti-Jo-1 autoantibodies. We investigated associations between prescription medication use and anti-nuclear antibodies (ANA) in a representative sample of the adult US population, based on all medications reported in the National Health and Nutrition Examination Survey (NHANES). Overall, ANA were less prevalent in adults who recently used any prescription medications compared with those who did not(OR=0.73),and several classes of medications were inversely associated with ANA, including hormones (OR=0.73), thiazide diuretics(OR=0.43), sulfonylureas(OR=0.41), and selective serotonin reuptake inhibitor antidepressants(OR=0.65). Positive associations with ANA were seen for loop diuretics (OR=1.72) in all adults, and for benzodiazepines (OR=2.11) and bronchodilators(OR=1.83) in older (ages 60) adults. Estrogens were positively associated with ANA in older women (OR=1.80) but inversely associated with ANA in younger women (OR=0.43). Novel ANA associations with medications, as well as unexplained inverse associations with certain medication classes warrant further research to clarify the possible roles of medications as risk and protective factors in the development of autoantibodies and autoimmune disease.